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Coverage Report

  1. Project Clover database Fri Nov 1 2024 11:46:37 GMT
  2. Package jalview.gui.structurechooser

File StructureChooserQuerySource.java

 

Coverage histogram

../../../img/srcFileCovDistChart5.png
43% of files have more coverage

Code metrics

16
46
13
1
301
156
25
0.54
3.54
13
1.92

Classes

Class Line # Actions
StructureChooserQuerySource 51 46 25
0.4444%
 

Contributing tests

This file is covered by 42 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui.structurechooser;
22   
23    import java.util.Locale;
24   
25    import java.util.Collection;
26    import java.util.List;
27    import java.util.Objects;
28    import java.util.Vector;
29   
30    import javax.swing.JTable;
31    import javax.swing.table.TableModel;
32   
33    import jalview.datamodel.DBRefEntry;
34    import jalview.datamodel.PDBEntry;
35    import jalview.datamodel.SequenceI;
36    import jalview.fts.api.FTSData;
37    import jalview.fts.api.FTSDataColumnI;
38    import jalview.fts.api.FTSRestClientI;
39    import jalview.fts.core.FTSDataColumnPreferences;
40    import jalview.fts.core.FTSRestRequest;
41    import jalview.fts.core.FTSRestResponse;
42    import jalview.jbgui.FilterOption;
43   
44    /**
45    * logic for querying sources of structural data for structures of sequences
46    *
47    * @author jprocter
48    *
49    * @param <T>
50    */
 
51    public abstract class StructureChooserQuerySource
52    {
53   
54    protected FTSDataColumnPreferences docFieldPrefs;
55   
56    /**
57    * max length of a GET URL (probably :( )
58    */
59    protected static int MAX_QLENGTH = 7820;
60   
 
61  138 toggle public StructureChooserQuerySource()
62    {
63    }
64   
 
65  0 toggle public static StructureChooserQuerySource getPDBfts()
66    {
67  0 return new PDBStructureChooserQuerySource();
68    }
69   
 
70  0 toggle public static StructureChooserQuerySource getTDBfts()
71    {
72  0 return new ThreeDBStructureChooserQuerySource();
73    }
74   
 
75  107 toggle public FTSDataColumnPreferences getDocFieldPrefs()
76    {
77  107 return docFieldPrefs;
78    }
79   
 
80  0 toggle public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
81    {
82  0 this.docFieldPrefs = docFieldPrefs;
83    }
84   
 
85  0 toggle public FTSDataColumnPreferences getInitialFieldPreferences()
86    {
87  0 return docFieldPrefs;
88    }
89   
90    /**
91    * Builds a query string for a given sequences using its DBRef entries
92    *
93    * @param seq
94    * the sequences to build a query for
95    * @return the built query string
96    */
97   
98    public abstract String buildQuery(SequenceI seq);
99   
100    /**
101    * Remove the following special characters from input string +, -, &, !, (, ),
102    * {, }, [, ], ^, ", ~, *, ?, :, \
103    *
104    * @param seqName
105    * @return
106    */
 
107  0 toggle public static String sanitizeSeqName(String seqName)
108    {
109  0 Objects.requireNonNull(seqName);
110  0 return seqName.replaceAll("\\[\\d*\\]", "")
111    .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
112    }
113   
114    /**
115    * Ensures sequence ref names are not less than 3 characters and does not
116    * contain a database name
117    *
118    * @param seqName
119    * @return
120    */
 
121  0 toggle static boolean isValidSeqName(String seqName)
122    {
123    // jalview.bin.Console.outPrintln("seqName : " + seqName);
124  0 String ignoreList = "pdb,uniprot,swiss-prot";
125  0 if (seqName.length() < 3)
126    {
127  0 return false;
128    }
129  0 if (seqName.contains(":"))
130    {
131  0 return false;
132    }
133  0 seqName = seqName.toLowerCase(Locale.ROOT);
134  0 for (String ignoredEntry : ignoreList.split(","))
135    {
136  0 if (seqName.contains(ignoredEntry))
137    {
138  0 return false;
139    }
140    }
141  0 return true;
142    }
143   
 
144  0 toggle static String getDBRefId(DBRefEntry dbRef)
145    {
146  0 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
147  0 return ref;
148    }
149   
 
150  0 toggle static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
151    {
152  0 Objects.requireNonNull(id);
153  0 Objects.requireNonNull(pdbEntries);
154  0 PDBEntry foundEntry = null;
155  0 for (PDBEntry entry : pdbEntries)
156    {
157  0 if (entry.getId().equalsIgnoreCase(id))
158    {
159  0 return entry;
160    }
161    }
162  0 return foundEntry;
163    }
164   
165    /**
166    * FTSRestClient specific query builder to recover associated structure data
167    * records for a sequence
168    *
169    * @param seq
170    * - seq to generate a query for
171    * @param wantedFields
172    * - fields to retrieve
173    * @param selectedFilterOpt
174    * - criterion for ranking results (e.g. resolution)
175    * @param b
176    * - sort ascending or descending
177    * @return
178    * @throws Exception
179    */
180    public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
181    Collection<FTSDataColumnI> wantedFields,
182    FilterOption selectedFilterOpt, boolean b) throws Exception;
183   
184    /**
185    * FTSRestClient specific query builder to pick top ranked entry from a
186    * fetchStructuresMetaData query
187    *
188    * @param seq
189    * - seq to generate a query for
190    * @param discoveredStructuresSet
191    * - existing set of entries - allows client side selection
192    * @param wantedFields
193    * - fields to retrieve
194    * @param selectedFilterOpt
195    * - criterion for ranking results (e.g. resolution)
196    * @param b
197    * - sort ascending or descending
198    * @return
199    * @throws Exception
200    */
201    public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
202    Collection<FTSData> discoveredStructuresSet,
203    Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
204    boolean b) throws Exception;
205   
206    /**
207    *
208    * @param discoveredStructuresSet
209    * @return the table model for the given result set for this engine
210    */
 
211  3 toggle public TableModel getTableModel(
212    Collection<FTSData> discoveredStructuresSet)
213    {
214  3 return FTSRestResponse.getTableModel(getLastFTSRequest(),
215    discoveredStructuresSet);
216    }
217   
218    protected abstract FTSRestRequest getLastFTSRequest();
219   
220    public abstract PDBEntry[] collectSelectedRows(JTable restable,
221    int[] selectedRows, List<SequenceI> selectedSeqsToView);
222   
223    /**
224    * @param VIEWS_FILTER
225    * - a String key that can be used by the caller to tag the returned
226    * filter options to distinguish them in a collection
227    * @return list of FilterOption - convention is that the last one in the list
228    * will be constructed with 'addSeparator==true'
229    */
230    public abstract List<FilterOption> getAvailableFilterOptions(
231    String VIEWS_FILTER);
232   
233    /**
234    * construct a structure chooser query source for the given set of sequences
235    *
236    * @param selectedSeqs
237    * @return PDBe or 3DB query source
238    */
 
239  65 toggle public static StructureChooserQuerySource getQuerySourceFor(
240    SequenceI[] selectedSeqs)
241    {
242  65 ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
243  65 boolean hasUniprot = false, hasCanonical = false;
244  65 boolean hasNA = false, hasProtein = false;
245  65 int protWithoutUni = 0;
246  65 int protWithoutCanon = 0;
247  65 for (SequenceI seq : selectedSeqs)
248    {
249  65 hasNA |= !seq.isProtein();
250  65 hasProtein |= seq.isProtein();
251  65 if (seq.isProtein())
252    {
253  65 int refsAvailable = ThreeDBStructureChooserQuerySource
254    .checkUniprotRefs(seq.getDBRefs());
255  65 if (refsAvailable > -2)
256    {
257  10 if (refsAvailable > -1)
258    {
259  8 hasCanonical = true;
260    }
261    else
262    {
263  2 protWithoutCanon++;
264    }
265  10 hasUniprot = true;
266    }
267    else
268    {
269  55 protWithoutUni++;
270   
271    }
272    }
273    }
274    //
275    // logic: all canonicals - no fetchdb
276    // some uniprot no canonicals: defer to PDB, user can optionally fetch
277    //
278  65 if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0
279    && protWithoutUni == 0)
280   
281    {
282  8 return tdbSource;
283    }
284  57 return new PDBStructureChooserQuerySource();
285    }
286   
287    /**
288    * some filter options may mean the original query needs to be executed again.
289    *
290    * @param selectedFilterOpt
291    * @return true if the fetchStructuresMetadata method needs to be called again
292    */
293    public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
294   
 
295  4 toggle public void updateAvailableFilterOptions(String VIEWS_FILTER,
296    List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData)
297    {
298    // TODO Auto-generated method stub
299   
300    }
301    }
  • Report generated by OpenClover v 4.4.1 on Fri Nov 1 2024 11:54:21 GMT using coverage data from Fri Nov 1 2024 11:53:58 GMT.
  • OpenClover is free and open-source software.